Mercurial > repos > devteam > sam_to_bam
comparison sam_to_bam.xml @ 12:9bd1568619cd draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
author | iuc |
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date | Sat, 27 Nov 2021 12:31:54 +0000 |
parents | 1e69848b596f |
children |
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11:1e69848b596f | 12:9bd1568619cd |
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14 @PREPARE_FASTA_IDX@ | 14 @PREPARE_FASTA_IDX@ |
15 | 15 |
16 samtools view | 16 samtools view |
17 -b | 17 -b |
18 -@ \$addthreads | 18 -@ \$addthreads |
19 -t '$reffai' | 19 -t "\$reffai" |
20 '$input' | | 20 '$input' | |
21 | 21 |
22 samtools sort | 22 samtools sort |
23 -O bam | 23 -O bam |
24 -@ \$addthreads -m \$addmemory"M" | 24 -@ \$addthreads -m \$addmemory"M" |
65 <param name="addref_select" value="history" /> | 65 <param name="addref_select" value="history" /> |
66 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> | 66 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> |
67 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> | 67 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> |
68 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> | 68 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> |
69 </test> | 69 </test> |
70 <test> | |
71 <!-- Test direct use of bgzipped reference --> | |
72 <param name="addref_select" value="history" /> | |
73 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" /> | |
74 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> | |
75 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> | |
76 </test> | |
77 <test> | |
78 <!-- Test with simple gzipped reference, which requires decompression --> | |
79 <param name="addref_select" value="history" /> | |
80 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" /> | |
81 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> | |
82 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> | |
83 </test> | |
70 </tests> | 84 </tests> |
71 <help><![CDATA[ | 85 <help><![CDATA[ |
72 **What it does** | 86 **What it does** |
73 | 87 |
74 Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands. | 88 Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands. |